Estimation of prokaryote genomic DNA G+C content by sequencing universally conserved genes

International Journal of Systematic and Evolutionary Microbiology
Pierre-Edouard FournierDidier Raoult

Abstract

Determination of the DNA G+C content of prokaryotic genomes using traditional methods is time-consuming and results may vary from laboratory to laboratory, depending on the technique used. We explored the possibility of extrapolating the genomic DNA G+C content of prokaryotes from gene sequences. For this, 127 universally conserved genes were studied from 50 prokaryotic genomes in the Clusters of Orthologous Groups database. Of these, 57 genes were present as a single copy in the genomes of 157 different prokaryote species available in GenBank. There was a strong correlation [coefficient of determination (r2) >95 %] between the DNA G+C contents of 20 genes and their corresponding genomes. For each of the 157 prokaryotic genomes studied, the DNA G+C content of the 20 genes was used to determine a 'calculated' genome DNA G+C content (CGC) and this value was compared with the 'real' genome DNA G+C content (RGC). In order to select the most suitable gene for the determination of CGC values, we compared the r2 and median mol% difference between CGC and RGC as well as the sensitivity of each gene to provide CGC values for prokaryotic genomes that differ by less than 5 mol% from their RGC. The highly conserved ftsY gene (median size 1...Continue Reading

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Citations

Feb 9, 2008·Emerging Infectious Diseases·Pierre-Edouard FournierDidier Raoult
Jun 23, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ewen F KirknessBarry R Pittendrigh
Jun 7, 2011·Annual Review of Microbiology·Pierre-Edouard Fournier, Didier Raoult
May 15, 2010·Systematic and Applied Microbiology·J Gaspar LorénM Carmen Fusté
Dec 17, 2008·Trends in Microbiology·Toïdi AdékambiDidier Raoult
Oct 27, 2007·The Lancet Infectious Diseases·Pierre-Edouard FournierDidier Raoult
Oct 25, 2011·International Journal of Systematic and Evolutionary Microbiology·Dmitriy V VolokhovVladimir E Chizhikov
Jul 5, 2008·International Journal of Systematic and Evolutionary Microbiology·Oleg MediannikovPierre-Edouard Fournier
Aug 5, 2008·International Journal of Systematic and Evolutionary Microbiology·Toïdi AdékambiMichel Drancourt
Sep 4, 2012·International Journal of Systematic and Evolutionary Microbiology·Shingo SatoSoichi Maruyama
Jan 8, 2015·Systematic and Applied Microbiology·Mincheol KimJongsik Chun
Sep 19, 2006·FEMS Microbiology Letters·Bernard La ScolaDidier Raoult
Jul 22, 2016·The Journal of Physical Chemistry Letters·Judit Morla-FolchLuca Guerrini
Mar 7, 2018·Archives of Microbiology·Dmitriy V VolokhovVladimir E Chizhikov
Dec 30, 2006·Electrophoresis·Ngoc-Phuc Hua, Takeshi Naganuma
Jan 16, 2007·International Journal of Systematic and Evolutionary Microbiology·Henrik ChristensenMagne Bisgaard
Dec 14, 2018·International Journal of Systematic and Evolutionary Microbiology·Dmitriy V VolokhovVladimir E Chizhikov

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